Hot, crowded rush-hour subways are in the future for thousands of Brooklyn riders — unless the MTA alters its Sandy repair plans, officials said yesterday.

In August the agency is planning to shut down the R train’s Montague tunnel under the East River for 14 months due to hurricane-damage repair, meaning trains won’t stop at six stations.

So 65,000 daily riders will have to hop off at Court Street and cram in to the 2, 3, 4 and 5 lines.

MTA officials and members of the Riders Alliance have proposed alternatives, including: running more trains on nearby subway lines, bus service between Downtown Brooklyn and lower Manhattan, and weekend ferries from Sunset Park to the Battery.

MTA spokesman Adam Lisberg said the agency will consider them.