Ubertis and Piettas made after 2000-2001 seem to be pretty good. Both shops re-vamped their tooling around then. Prior to that they were getting problems with basic metallurgy, so...yeah, new or at least newer is good.
The Beretta Stampede is an Uberti with a transfer bar ignition grafted in. It's still more traditional than a Ruger as it loads on the half-cock, but the reliability is a step down from the no-safety Uberti variants.
Pietta also does a transfer-bar equipped gun. It's fairly rare, sold only by Heritage which calls it the "Big Bore Rough Rider":
http://www.heritagemfg.com/site/department.cfm?id=52
Final finish and assembly is stateside from Pietta parts. Taurus recently bought Heritage and I for one suspect they'll want to keep the deal with Pietta going and possibly expand the program if possible, because Taurus' own Brazilian-made SAA-near-clone-with-a-safety (Gaucho) was a total failure.
A Pietta is a decent alternative to Uberti and otherwise very similar. A lot of the SASS guys are happy with the ones imported by EMF as the "Great Western II" or more recently by Cimarron which used to be an Uberti-only shop but added Pietta of late. Pietta's CEO competes in European SASS matches as "Alchemista" and there's a Pietta model of that name set up for guys with big hands.
Both Pietta and Uberti have lower-slung-hammer models available now that SASS has legalized the use of the Ruger SuperBlackhawk hammers "or similar" in all aspects of competition ("main match"). At first they were a mounted-only thing.
What else...
Uberti's best possible fit and finish under their own name is called the "El Patron". They also sell that finish level to Taylor's & Co. who sells it as the "Running Iron" or "Smoke Wagon" depending on options. Cimarron sells that finish as the "Evil Roy" and possibly others, with the Evil Roy tuned up internally in-house.
Longhunter's Shooting Supply in turn is a gunsmith and gun sales operation that sells pre-tuned guns including Rugers and the Taylor's high-end Ubertis. One of those Ubertis pre-tuned by Longhunter is probably the single best Italian SAA type you can get, matched only by the Evil Roy which is more money.
http://www.longhunt.com/
Hmmm...looks like he's also tuning some Cimarron models so that might be worth looking at.
You might also note that he's tuning Rugers. A Ruger New Vaquero is still a fundamentally better gun than anything coming out of Italy, if you care about toughness and performance more than looks. In his list of pre-tuned Ruger services, checking the throats isn't listed BUT if you call him I'd bet he'd be willing to go there for a slight cost. That would, in my opinion, get you the very best SAA-class gun possible this side of a grand-plus worth of USFA or Colt or two grand worth of Freedom Arms '97-frame.
Remember: any Ruger mid-frame (New Vaquero, Montado, 50th Anniversary 357 Blackhawk Flattop or the 44Spls fixed or adjustable) have cylinder chambers that were all bored with the same bit/reamer set. Large-frames from 2007 forward got the same improvement...you can ID those by the "lawyer's warning label" on the barrel of the large-frame guns: under-barrel warning means new enough to get the improved cylinder, side-barrel means too old. If it has uniform chambers that's a great start. In 45LC you're correct, there's a risk the throats will be tight but it's easily fixed and once you do accuracy is generally a dream.