I commute to Brooklyn from Lindenhurst (Suffolk County) and the train is the best bet. The caveat being you need a folding bike. LIRR sells bike permits but still doesn't allow any non folding bikes on peak trains. No permit needed for a folder. They consider the folding bike luggage and therefore do not restrict it.

I've found Long Island is not very bike friendly with regards to the drivers and road infrastructure. I actually feel safer riding up 4th ave in Brooklyn than Sunrise Hwy in my town.


Hope this helps, good luck!