I've found (on my keyboard) attempting to block the shot does very little to lower the % of threes that go down, unless you actually connect on the block.
I have been experimenting and from what i have found the best way of lowering the % of these shots that are successful is to put your hands up, by pressing the takecharge button just as the player is about to shoot.
This reduced one teams 3P% dramatically, I held them to 1 from 10 for the rest of the game after i started doing it as opposed to the usual 30 or 40% of contested shots (may i repeat how annoying it is the amount of contested shots that connect in this game). 2 of the 10 attempts even airballed (using Kenny Anderson and Robert Pack as the defenders, neither of which are very tall).
This method works!