Depending on how busy it could take anywhere from 30-60 minutes or more to clear customs and get baggage. To get to Times Square: take the NYAS bus ($15) to Port Authority (two blocks from Times Square) which leaves every 20 minutes from each terminal and takes about one hour OR take Airtrain from your terminal to Jamaica Station and then E subway to 42nd St./Port Authority ($7.25), takes about 1-1/4 hours.
Depending on how busy it