Hi, I will have the following situation: will be in Japan on business and will have to work in company's office in Tsukuba. However if at all possible I would like to stay in Tokyo therefore commute will be involved. I will be staying near Shinagawa station.

Most logical commute seem to be Shinagawa to Akihabara then to Tsukuba on Tsukuba express. Problem is Tsukuba express doesnt have reserved seating and have watched horror footage of what may happen at Japan rail stations at the rush hour, this is my worst preferable option (cost Y1,310 one way)

Another option is to take JR Yamanote line to Ueno and then Hitachi Ltd express to Tsuchiura.. from Tsuchiura taxi to Tsukuba (was advised that taxi takes 20-30 minutes and costs ~Y5,000). So total cost will be ~Y7,800 one way). It takes about the same time as Tsukuba express option but obviously have reserved seating.

Am I missing something and there's other option?

AX

Though Tsukuba Express does not have reserved seating, I think it is not so hard to find a vacant seat in the morning. This is because, 1 Akihabara is its starting station. 2 Most of the people commute from suburbs to central Tokyo.

However, the Shinagawa to Akihabara run on the Yamanote Line *will* be very crowded on a weekday morning.

Another option is to stay around Tokyo Station. There is a regular JR bus service from the Yaesu side (east side) of the station to Tsukuba, which stops at several places in the Tsukuba area. It takes about an hour and costs 900 - 1,200 yen, but you get a guaranteed seat.

However, I have ridden the Tsukuba bus on a day when it took an hour just to reach the edge of Tokyo and enter Chiba-ken.

Ask around and see if there is a bus that runs to one of the stations that is served by the Tsukuba Express. The labels on the fronts of the buses are in Japanese only, for the most part, but I have lucked out at times and found one that was going precisely where I needed to go.

They usually run between major train stations.

As other mentions, your major problem is the transit within Tokyo, not the one to Tsukuba because you are traveling in opposite direction of anybody else.

Just a brain storming : When I flew Haneda and enter Tokyo with Keikyu, most people got off at Shinagawa station. It probably feasible to do

Shinagawa => Asakusa (Toei) >> Walk >> Asakusa (TX) => Tsukuba

just to avoid JR.

In addition for just Yamanote line, you should check if it is feasible (aka space avaliable) to do Keihin-Tōhoku line instead. In theory shinagawa is the first major station in Tokyo and train should start free-ing up (as people change train to Yamanote line)

Or, if its easier, book an hotel in Ueon / Akihabara area instead

Note, though, that the TX and Asakusa Line stations are really far apart and you have to go several blocks through Asakusa to get between them. Staying in Akihabara seems like a really good option -- or, alternatively, stay in a nice place on the east side of Tokyo Station and take a cab to/from the TX side of Akihabara.

Between Shinagawa and Tokyo:

OP appears afford to take a cab roundtrip everyday, how about taking a Green Car seat? It cost 750 yen extra for one way between Shinagawa and Tokyo.

Between Tokyo and Akihabara:

It is the less crowded direction of the rush traffic and takes just 4 minutes. So, this portion will not be a big problem, IMO.

Perhaps you could stay at the Asakusa View Hotel, which is very close to the Tsukuba Express Asakusa Station.

There's Remm Akihabara that's practically part of the Akihabara station complex, or Akihabara Washington Hotel that's right across the street.

The OP seems to have decided on staying near Shinagawa Station though.

Given that Shinagawa is on the southwestern side of Tokyo and Tsukuba is to the northeast, this is sub-optimal to say the least. I'll second Akihabara as the obvious place to stay.

Re: the Toei Asakusa line, while it doesn't get as packed as Yamanote, I'd still expect standing room only during rush hour and it's a fairly lengthy ride.

Unfortunately we dont have much choice in terms of what hotels we can used for stays. this is exacerbated by the fact I dont know geography of Tokyo much to comprehend what option is better wrt Tsukuba commute.
Other hotel options for dates of my visit are:

Sheraton Yokohama bay
Intercontinental Yokohama
Imperial hotel Tokyo
New Otani Hotel Tokyo
Okura Tokyo Hotel
Pacific Hotel Tokyo

Anything you see from the list above that may be a best option to live while commutting to Tsukuba?

AX

I'd go with the Imperial if those are your only options. It's much closer to Akihabara -- straight shot on Hibiya Line out front, shorter hop on Yamanote if you walk a few blocks, and the taxi ride should be 1,500 yen or so.

I agree with that suggestion.

The Imperial is practically on top of Hibiya subway station (direct line to Akihabara), and it's only a couple of blocks from the Yurakucho JR Station on the Yamanote Line. It also fronts on Hibiya Park and the Imperial Palace. You can't visit or even see the actual palace from the publicly accessible walks, but the grounds are pleasant, and the small museum shows a rotating collection of works from the imperial family's private collection.

I'd take the Yamanote, because a large number of people will get off at Tokyo Station (the next one after Yurakucho) and because after you leave Tokyo, Akihabara is the second stop. The sequence is Yurakucho, Tokyo, Kanda, Akihabara.

If you take the subway, it's Hibiya, Ginza, Higashi-Ginza,Tsukiji, Hatchobori, Kayabacho, Ningyocho, Kodenmacho, Akihabara.

For your leisure hours, I'd suggest buying a Tokyo city guidebook--there are several on the market--and Kodansha's Tokyo City Atlas, which is what I consulted in order to refresh my memory on the location of the Imperial and the sequence of subway and train stops.

Thanks for the info. How long you reckon a taxi ride will be around 7am from Imperial to Akihabara stn?
AX

I would guess 15 minutes. It's only 3 km or so, so it shouldn't be horribly long even if traffic is bad.