I'll be attending KCON (a korean pop music festival) in Chiba that occurs from Fri April 13- Sun April 15. The concert is in the evening for all three days. Seems like it takes about an hour to get from Tokyo to Chiba by rail. My plan is to arrive in Tokyo around April 6 and depart Monday April 16. I initially had planned on staying all days in Shinjuku/ Shibuya area but wanted to get people's opinion first.

KCON 2018 JAPAN

No idea about KCon, but I have been to plenty of music festivals in Europe.

Staying locally for those dates at a hotel full of other concert goers (perhaps even a few of the Artists and their entourages) can really enhance the experience. At least that what I've found.
Are there no activities and events for fans going on? Meet ups and fan club socials?

From the concerts I've been too at Makuhari Messe, I find other than some after parties, there isn't much of a concert goer atmosphere in the surrounding area. But at the same time korean pop concerts tend to attract a different crowd than I'm used too so it may be different. I will say though, if you stay near Makuhari Messe, you are going to be all in for the concert experience because there really isn't much out there other than the convention center, a mega shopping mall and a baseball stadium.

KCON does have a full day of events planned for each of the three days, but I'm really not interested in those events so will just be showing up for the concert and dinner beforehand. So the better choice would be to stay in Tokyo and take the one hour train ride there and back all three days?

Were the after parties you attended planned or just organic events that popped up at the local bars and clubs?

Definitely. Makuhari is not an interesting place to stay.
Stay somewhere near a Yurakucho Line station, so that you can ride the Yurakucho line to Shin Kiba, then change to the Keiyo Line.
(Or stay near the southern end of Tokyo Station - which is where the Keiyo Line platforms are)

Staying in Shinjuku/Shibuya for a festival that takes place at Makuhari Messe in Chiba is a way to make your life difficult. Tokyo is a big city, but it will seem even bigger if you stay on the west side of central Tokyo and travel to a city that lies to the east of Tokyo.

You might think that you want to stay in Shinjuku/Shibuya for the night life, but if you travel from there to Chiba for concerts in the evenings, you will

1) Probably be riding at rush hour for at least part of the trip and on the outward-bound trains along with all the other people who work in central Tokyo and live in the eastern bedroom communities
2) Missing the main part of the night life in Shinjuku/Shibuya anyway

I agree that Makuhari Messe is not the most fascinating place to spend the day, but at least stay somewhere on the east side of Tokyo. As long as you are on a train or subway line within Tokyo, you should be able to sightsee during the day.

Or else just resign yourself to shopping mall boredom--although you wouldn't be very far from Disneyland and Disney Sea on the Keiyo Line-- during the days of the festival and enjoy Tokyo before or after.

If you ate only going at night, then definitely do not stay near the convention center. I'd go on Google Maps and check transit times to determine the best place to stay.

For after parties, there are no local bars or clubs. Just Hotel Restaurants, Shopping Mall Restaurants and Hotel Ballrooms. The after parties were planned in advance and held in the ballrooms.