The MTA approved across the board fare increases for March 1, 2008. Your monthly subway goes from $76 to $81. Your LIRR monthly goes from $130 to $135, a mere 3.8 % increase (the low end of the scale).
Also, the R train will run all night - it currently goes out of service in the overnights and the E handles local stops.
I implore you - try the LIRR. Twelve minutes - no exaggeration. It's not perfect and the LI slobs will drive you nuts. But the envious look they give you when you get off at the first stop and they have 75 minutes left is priceless. No homeless, no begging, no roving gangs of youths looking to make you the star of their next You Tube production. If you work anywhere near Penn Station, give it a shot when the weather gets warmer.