The subway doesn't go to LGA. You need the bus first. Take the Q33 to the Roosevelt/Jackson Heights subway.

http://www.mta.info/

I've taken the supershuttle from JFK to Times Square before, I think it was $15 ish

http://www.supershuttle.com/

Also the NY Airport Service Bus does runs to Manhattan...

http://www.nyairportservice.com/

And to Newark, $14 on Olympia trails

http://www.coachusa.com/olympia/


And for a bunch of other airport transport links
http://www.geocities.com/capitolhill/5355/airporter.htm