There are a lot of buses that run through East Harlem but those are not at all useful going up and downtown. You should only use them for crosstown jaunts because they are painfully slow. You can look up stops and schedules on the MTA website. As far as trains, unfortunately, there's only the green line that runs uptown on the east side. It runs along Lexington through East Harlem which is nice because it's central to all of the neighborhood. The 4 and 5 of the green train are pretty fast so the situation isn't terrible but that is the only option so you'll probably have to switch trains at Grand Central or Times Square if you need to get somewhere on the west side . . . which can take an hour.
