I feel more impressed with Alabama's but it could be just because it is the more recent run.
In the three years for each:
Alabama beat more ranked opponents
Nebraska didn't lose at all.
Both teams had impressive performances in Bowl Games in their second and third years but shaky or less dominating wins in their first NC year.
I happen to think Bama's is the better of the two dynasties just because I respect the competition that they have faced more than the teams Nebraska faced. I think that It's much tougher to build a dynasty in a conference like the SEC where four other teams had won National Championships in the past decade or so (Auburn, LSU, Tennessee and Florida) than it is in the Big 8 where the only real consistent competition came from OU and only occasionally from Colorado.
You may respect their competition more, but it's not like they came out unscathed. They
lost to that competition. Nebraska went undefeated and nobody can say that Nebraska would've lost to those teams too... you just can't say that.
I can just say that. Manziel and a bunch of young Aggies would demolish the 1994 Nebraska football team if they played today. It wouldn't even be close. 
But really you do make a good point. There is something to be said for NU not losing a single game during that period, and while they went undefeated they also, in my opinion, didn't play as good a competition as Alabama has but NU won those games like they should have...by a lot but then again Alabama's points for/against average is damn good too. I guess it comes down to how you want to measure it.
There is not definitive way to determine which had/has the better dynasty. The answer to that question is going to vary from person to person. I'm comfortable just letting them stand how they are, saying that both were amazing sets of teams and sitting back to see how Alabama plays the next few years out.
