Is the regular MTA and the long island rail road the same price?
No, MetroCard are not accepted on Long Island Railroad and Suffolk County Transit, however it is only accepted on Long Island Bus which does not go to Bay Shore. Best chance is to take bus to Jamaica Station (Zone 3), then purchase ticket to Bay Shore (Zone 10) from Vending Machine which cost $13.50 peak/$9.75 off-peak. If you want to avoid the LIRR, you can but buses take long time, purchase Unlimited MetroCard. From Jamaica-165th St bus terminal, take N6 (Early Morning, Limited is available.) Take N6/N6 Limited to Hempstead Transit Center. Transfer to N72 bus to Babylon RR station, transfer is 25 cent, however some drivers will give you transfer free if you are connecting to Suffolk County Transit. If you cannot get transfer from Long Island Bus, you can paid $1.50 in cash (US Dollar Bill accepted) Suffolk County Transit transfer is 25 cent and up to two connecting buses. From there you can catch either S40 or S42.