There is no reliabilty issues with a 347 vs a 331, you can not predict how long each will last, built correctly you will not have any issues.
I suggest a 331, you can get a more blower friendly compression ration with a shelf piston over the 347. Also unless you go with a 5.315" rod based 347 you get a slightly taller compression height piston with the 331.
I build a lot of both, you will not have any issues. If you are going to put better then stock internals in the motor definitly go with the stroker. If you are using a stock block, you'll break the block before you hurt a good cast crank, forged rod, forged piston combo. If you are planning on moving up to a DART SPortsman $1800 or Iron Eagle $2100 then I would suggest going with a Forged crank so you can have a near bullet proof assembly, with a rod bolt upgrade you can take the HP rating from about 800 to 1100+.