Any suggestions on where we can kill a few hours at the airport after we land. Our flight lands at Terminal 3 around 6am & I have early check-in at the hotel but that is only at 11am. Is there an arrival lounge or someplace we can have breakfast before leaving for the city around 10am?

You can kill time in Tokyo

What can we do that early in the morning in Tokyo?

It's not a cheap option, but you could visit the airport onsen and soak in a bath while watching planes land:
https://www.shopping-sumitomo-rd.com...userguide.html

You can judge whether the breakfast menu there is to your taste:
https://www.shopping-sumitomo-rd.com...nt2/menu_m.pdf

But if you're encumbered with luggage, the easiest thing is probably to head straight into central Tokyo, drop your things at the hotel, and find something to distract you in the area, as recommended above.

Will take a look. Thanks.

I would head to the hotel and drop your bags there. Then you can kill a couple of hours without dragging your bags along with you. I've never had any issues with leaving the bags with the Front Desk and often the bags would be in my room before I actually checked in.
Depending on where you're staying the train to town won't be the full rush hour sardine can for at least part of the trip. The Keikyu and the Monorail both start running around 6am so you shouldn't have any issues getting into town. By the time you get to town most of the coffee shops will be open. Also there might be some of the shops open landside for the morning departures, but most of them don't usually open until later in the morning, much more to do in town.

As luck would have it, I just got a notification informing me that our flight this evening is delayed by over 4 hours so now the estimated landing time is 10:10am tomorrow morning. Couldn't have worked out better. :)

Thank you to everyone on this thread for their wonderful suggestions. We had a great trip & can't wait to go back.

Just a few pointers that may help others looking to plan a trip:

In Tokyo we got the unlimited 3 day metro pass that is available for foreigners. This helped us explore the city in the best way possible.

We found Ginza to be a great base to get around the city. There was enough around our hotel to keep us busy as well so the location couldn't have been better for us.

In Kyoto we opted to get the 3 day JR Kansai Mini Pass. This way we split our 7 days by spending 4 exploring Kyoto & spending a day each going to Nara, Osaka & Kobe.

For 3 out of our 4 days there we got the subway & bus one day pass & that worked out great for us.

We found the Shijo area to be a great location for us. The subway was a 5 minute walk from our hotel & the bus stop was right opposite the hotel. We also explored the area on foot quite a bit.

We were told that most things would be closed for a few days between the 31st of December to the 2nd of January but besides a few large stores & small number of tourist attractions, everything else was open. We spent the 1st & 2nd visiting a number of temples, doing a samurai & ninja experience (which was one of the highlights of the kid's trip) & walking around Nishiki & Pontocho Alley.

On the last evening before our flight we took the last limousine bus to the airport & stayed the night at the airport hotel.

All in all, it was a fantastic first visit to Japan. There is so much more we want to explore but our 2 weeks only allowed us to do so much. We plan on going back again next year.