Well, a few things going on here.
I was skipping Miller's numbers this year for no good reason. So yes he's better this year, though league SV% has continued to go up.
The new wisdom is that quality of team defense doesn't affect goalie's SV% as much as you would assume. Obviously it affects GAA as they face more shots, but goalies largely save the same percentage of them at the NHL level. So, Miller seems to be getting a bump because his team isn't good but research shows that doesn't really matter -- over the large sample size of a season or career, all shots are more or less created equal.
To further suss this out you can remove power plays from the equation, when teams are definitely more likely to get quality shots off.
Extra Skater has these stats back to '11-12. SV% rankings for starters at even strength:
2013-14: Miller 20th, Halak 17th
'12-13: Miller 17th, Halak DNQ*
'11-12: Miller 17th, Halak 2nd
*Halak only played in 16 games in the shortened season and his ESSV% was a very poor .909. If you lower the GP threshold to 12 GP get Halak in, he is 46th in the NHL and Miller drops to 25th.
So at even strength Miller has consistently been an average NHL starting goalie, while Halak has been anywhere from awful to second-best in the league.
In all situations, Halak is about .001 better, leaving out their first couple partial seasons. This year, Miller is 10th in the NHL in SV%, and Halak is 14th. Personally I think you can give Miller a plus for consistency and for having held up under bigger workloads in his career, but as I said I don't see the evidence that Miller is any more than an above-average starter at age 34, which Halak basically is too at age 28. Miller had a great season in 09-10 (2nd in NHL in SV%), but Halak had great seasons in 11-12 (7th in the NHL in SV%) and 09-10 (5th) and we remember what he did in the 09-10 playoffs.
Edit: Your point about the Sabres being better with Miller is kind of a tautology...we know that Miller is better than Enroth. Enroth has a career .912 SV% so his .906 this year isn't really noteworthy, and of course the Sabres are going to win more games with a better goalie playing.
Edit #2: Some more stats from earlier this year.
http://www.stlouisgametime.com/2014/1/3/5271938/is-miller-better-than-halak