I can't say I know much about bike rental in the city, Bike and Roll seems
like it does a brisk business and they have a lot of locations. As for
shops, I like the folks at NYC Velo. Their shop's not really interesting
outside of a normal well stocked bike shop but their repair staff is nice
The Hub and Waterfront Bikes are both great for rentals. The Hub is also
one of the city's better shops for practical city bikes and is worth a
visit:
http://www.hubcycles.com/
http://www.bikeshopny.com/
Other interesting shops to check out:
http://www.redlanternbicycles.com/