Most of my suggestions have already popped up here.

Big Lou's in LA is worth checking out and it's in handy walking distance of a TRU and Target and near a bus route. I got around LA fine just using public transit (but I think I had the bulletproofness of youth because when I think about it now I'm not sure I'd highly recommend it). Everything is far apart though. The nicest part of LA I found was Santa Monica, would stay there if I went back.

Unlike NY were you can walk or subway it anywhere you need to get to. Midtown comics in NY was good, but also check out the New York store of Forbidden Comics (near Union Square subway station). While in New York if you're going to see a Broadway show go to the TKTS booth for discounts of up to 50% for same tickets. The Staten Island ferry is a good way of seeing the Statue of Liberty without the massive queues to actually visit the island.