What subway do you take from Penn station to Allen street?

Take the Downtown A-C-E (the blue line) from 34th Street-Penn Station to West 4th Street.

Transfer at West 4th Street to the Downtown F train (of the B-D-F-M, the orange line) to 2nd Avenue-Houston Street or Delancey-Essex Street.

Allen Street runs north to south from Houston Street to just below Canal Street. The 2nd Avenue-Houston Street Station will drop you off a couple of blocks west of Allen Street. The Delancey-Essex Street Station is three blocks east of Allen Street, and three blocks below Houston Street.