technically, manny's is closed and is now part of sam ash... i went up there a couple of weeks ago, and i had no idea it had closed. but it's still there, it's just a sam ash place now. pretty much the same, though... except i think they got rid of the drum part upstairs. Rudy's is another quality guitar spot with a bass room upstairs, mostly vintage and used stuff, that's also on 48th street, across from Manny's/Sam Ash. the guitar center in manhattan (on 14th st.) has a pretty decent vintage room, too... although i hesitate suggesting going to guitar center, because it's a really annoying place to be (although i find myself spending way too much time in there for work).
As far a clubs go, it depends what you're into. Jazz place- go to the Jazz Standard. it's definitely the most family club, and it has some amazing food. there's always the village vanguard, that's probably where you'll see the best music. i'd suggest staying away from the blue note... i've had some bad experiences there. if you want to see some good local rock stuff, there are some good clubs on Bleecker st. between laguardia place and 6th ave, like the Bitter End.. that neighborhood is pretty cool. definitely get's rowdy around there on the weekends, but it's not nearly as bad as it used to be. i lived there for 2 years.
anyway, my suggestion would be to go online and check the schedules for clubs and see if there's anything going on that you're interested in.
i'll definitely second the museum thing. we have some of the best in nyc. MoMA is probably my favorite, depending on what's going on though. Check the upcoming exhibits.
use yelp.com to check out reviews of places (restaurants especially), i do it all the time.
and go to shake shack. preferably the original one in Madison Sq. Park, because it's the best cheeseburger you will ever have. i promise.
