Brownstoner had this to say about getting to Brooklyn Flea:

Just a quick note to check the weekend subway changes on the A/C and G lines this weekend at the MTA site before heading out to Fort Greene. Seems like the F is running on the A/C line from Hoyt-Schermerhorn to the Flea (use the Lafayette Ave. stop, 5 minutes away), and buses are replacing the F/G from Bergen St. to 7th Avenue. The G is stopping normally at Clinton-Washington Ave., which is literally a block from the Flea (use Clinton Ave. exit).

Your other subway option is any train that goes to Atlantic Ave.-Pacific St., which is at the intersection of 4th Avenue and Flatbush Avenue. The 2/3, 4/5, B/D, M/N/Q/R and Long Island Railroad all stop there–the Flea is a lovely 10-15 minute stroll from there.

Check out this map to find your way. It shows all the subway stops mentioned above.