The chan is for channel in both 2ch and 2chan. It's kept straight like this:

2ch = ni channel (two channel)

2chan = futaba channel (two leaves channel, kind of hard to explain, but in Japanese numbers are pronounced differently depending on what they are counting. Sort of like the difference between saying "two channel" and "second channel".)

4-ch's name hasn't been announced by it's creators, so I'm not sure how they want it to be said.

4chan = yotsuba channel (similar to futaba, but four instead of 2) Personally, I think it's confusing for an English language site to use such an un-obvious Japanese pronunciation, but if you are familiar with the Japanese boards, it makes sense.