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Two Ruger new Vaqueros both 45 both with reamed cylinders one shoots 5 shot 1 inch groups and the other 3 inch groups any ideas?

Every gun is different. Time to work up a load it likes.

Just like recumbent said "every gun is different" and sometimes headscratchingly so....

Assuming both cylinders have been reamed by the same person/reamer then you're consistent there (and I really like the word consistent). Then you get to play with differences between barrels. Just say you're lucky and the barrels are also similar in having no thread choke, what's left is cylinder alignment and a couple other possibles. That, or one revolver just doesn't "like" the same load (which is probably all that is going on).

I would love to have a box of loaded ammo I can use between different same caliber revolvers, but personally I tend to use different revolvers, well, differently. Play with your charges and that might do it for any number of reasons, or change bullets and start the process all over. Sounds like more experimenting is in order for both or have different ammo for each.

I'm a weird knothead in that I enjoy the chase and a challenge makes me happy (though I'd never admit it out loud). Casting bullets adds to the aggravation and enjoyment as you can play with hardness along with overall shape, weight, length, etc. The above said, a good LFN style bullet cast with COWW and pure lead (I use 2 parts COWW 1 part pure lead mostly) and sized where the loaded ammo will drop in with no hard push will shoot good as long as you're not dealing with an obvious gun problem. I've yet to play with a 45 Colt that doesn't shoot well with either HS6 or H110. HS6 has been my go to for my enjoyable loads at somewhere around 950-1000 fps. I don't load my 45 Colts very light but don't need them to be 44 Magnum killers either.

Just my rambling answer to your dilemma. I say dilemma and not problem as I consider the place you are at is still enjoyable. You will just have to play some more.

As noted,, despite the appearance of being identical,, they are different machines. As such,, the cheapest & easiest thing is to play with reloads.
As noted,, sometimes a single load works well in many different guns,, while some loads never work but in one gun.

Your post left out a lot of info.
Factory ammo or reloads?
Cast or jacketed?
If cast,, have you slugged the bore?
Thread choke issues? Have you checked for that?
And as noted above,, who & how were the cylinders reamed?

I thank you all Back to the reloading room I go.

At this stage it sounds like the one shooting the larger groups could have thread choke. Time to slug both barrels. One barrel could need a larger diameter bullet or fire lapping. Be sure to clean the bore squeeky clean when going from jacketed to cast and vice versa.
You did not say how far your target is from where you are shooting. If 25 to 50 yards a one inch group is wonderful. A three inch group is not that bad, but more than likely can be improved. Like I said though I would concentrate on the one shooting the larger groups. It may need a larger bullet or fire lapping to get it to where you want it . Good luck.

I am cut of the same cloth....now sending out five cylinders split between our two member friends specializing in throat sizing. Pin gauges will tell you if you need that. Pin gauges will also detect thread pinch....you don't have to guess at it. Fire lap if necessary after throat work.
Be certain of your barrel slugs. Take several and re measure. Figure your bullet diameter based on the usual formula discussed here and elsewhere.
For testing, use a load that you and others have found to have confidence in. As long as it is carefully assembled and crimped, use that reload for all of the testing. Shoot all of the guns with the same load and several different distances under the same or different
conditions. The targets will tell you a lot. Don't worry about your group sizes until you have gotten your revolvers squared away mechanically. Wouldn't hurt to install a better base pin before you do all of this.
The forcing cone alignment consentricity with the bore axis can be estimated by lightly turning an eleven degree cutter lightly. Custom made snug pilots would be best to do this, and for the actual cutting. You will need to buy or rent the forcing cone depth gauges from Brownells or other to see if you have enough material to re cut at all. I have a five degree cutter from Pacific Tool, but just found that it is too long to go inside the frame....will work with them on that.
Overly deep forcing cones will never be accurate no matter what size bullet, and just lead your bore down by the breach. Doing all of this blue printing ahead of time will save you a lot of time in working up individual reloads for each gun.
Next, if you feel up to it, fit a Powers oversized cylinder latch. At that point I would work up your loads. By then if you have worked at it in this order, the gun deserves a quality action job or Powers hammer and trigger and custom sights. Great fun and very challenging. Few will understand why we would go to all this trouble, but who cares.