The run counts, this scenario is spelled out in the rulebook
APPROVED RULING: One out, Jones on third, Smith on
first, and Brown flies out to right field. Two outs. Jones tags
up and scores after the catch. Smith attempted to return to
first but the right fielder’s throw beat him to the base. Three
outs. But Jones scored before the throw to catch Smith reached first base, hence Jones’ run counts. It was not a force play.