st marks is highschool kids. it's not like it's dangerous- just annoying, in the way hs kids are annoying (thoughtless, loud, inconsiderate, dirty... annoying). head-shops, pizza parlors, t-shirt shops, etc- not really stuff for grown-ups... but the stretch from A to 1st is better than the other two blocks. reagardless- its a non-issue... it's only a couple of blocks, easily avoided or quickly walked through.
citibikes- yeah, you've got it. with the day pass, you're good for 30 minutes at a time before having to dock the bike.
with the year pass, I have to wait 2 minutes before taking out a new bike... probalby the same with the day pass. I don't think this is going to be an issue for you- during the day there are lots of bikes available in most places. rush-hour is when bikes get harder to find and to dock. fwiw- on A and 7th, between 7-10pm, they have a valet constantly clearing out docks- so if you find yourself looking, just go there instead. (edit... tbh, I'm not sure what the etiquette is on docking and taking out the same bike, especially if somebody's waiting... I've seen people "claim" the bike they've just docked- and I'm not going to argue with them- seems a little dickish to me, though)
also- there are finally stations all the way up to 110th street on both sides of the park, so you can conceivably ride up to the museums and central park.
for a sense of time, fwiw- takes me 20ish minutes to get from Houston & A up to work at 39th and 5th... but I ride fast (as fast as the citibike allows, which isn't very).
9th st is a good west-bound bike lane... 10th is good for heading east. 1st ave has the only legitimate bike lane on the east side (goes all the way uptown). 2nd ave comes down, but only starts below the midtown tunnel (33rd-ish street). 8th and 9th aves are dedicated up/downtown bike lanes on the west side, 6th ave is the oldest and sketchiest uptown bikelane, narrow and rife with doubleparked trucks/uber, pedestrians, wrong way people... sucks.