What subway do you take from Penn Station to get to East Houston Street?

You can take the Uptown E train (of the A-C-E, the blue line) from 34th Street-Penn Station to 53rd Street-Lexington Avenue. Transfer is available from this station to the 51st Street Station on the 6 train (of the 4-5-6, the dark green line). Walk through the tunnel that connects the two stations, and take the Uptown 6 to 68th Street-Hunter College (at Lexington Avenue).

There's another route that requires less walking, but requires you to go Downtown and then back Uptown: take the Downtown A, C or E from 34th Street-Penn Station to West 4th Street. Transfer at West 4th Street to the Uptown F (of the B-D-F-M, the orange line) and take the F to 63rd Street-Lexington Avenue.