Both ways worked. Using the first method, like this:

$seed1=range(1,10000);
$A=maple("RandomTools[SetState](state=$seed1);LinearAlgebra[RandomMatrix](4,4,generator=-9..9)");
$seed2=range(1,10000);
$B=maple("RandomTools[SetState](state=$seed2);LinearAlgebra[RandomMatrix](4,4,generator=-9..9)");

The second method is about the same difficulty but seems a little cleaner:

$seed1=range(1,1000);
$A=maple("randomize($seed1):LinearAlgebra[RandomMatrix](4,4,generator=-9..9)");
$seed1=range(1,1000);
$B=maple("randomize($seed1):LinearAlgebra[RandomMatrix](4,4,generator=-9..9)")

@Alex Smith: If you aren't setting the seed value for this second method, what are you setting? They both look very similar.

If you just try to reinitialize seed1 the second time (instead of creating a seed2) both matrices will be the same.