I've owned quite a few of both. The M-39 is generally better put together, but there are exceptions. The M-39 was created to replace the assorted rifles that had been built and issued to various SA and Civil Guard units, and was probably seen as "top of the line" at the time. But the M-91 continued to be built during the Continuation War and was only phased out as the Finnish M-30 (their 91/30) came on line because they had so many captured 91/30's to work with. The M-91 nevertheless was NOT a rear guard weapon. It saw a ton of active service in all the wars.
Accuracy-wise, the M-39's big drawback is its huge birchwood stock coupled with a lack of aluminum sleeve. This means the stock tends to impinge too much on the barrel. You will frequently find a bunch of shims inside M-39 actions that were put there in an effort to ease tension on the end of the barrel. Any warping of the wood since then may have caused the rifle to go out of whack again. As a result the M-39's tend to be more variable, but the best of them are excellent.
The M-91's tend to be a bit more beat up and seem to have been put together a little faster. But the design is very Russian and more forgiving. The front end of the stock uses very thin wood, which ironically seems to crack LESS than the beefier M-39 stocks. This means it doesn't warp against the barrel as hard. There may be some contact, but it's a GOOD kind of contact set at the arsenal to maximize barrel harmonics. An M91 out of its stock will often have DECREASED accuracy.
On balance, I'd call it about a tie. But the Finn M-91's I've owned have been a little more consistently good whereas I've had some frustraiting M-39's. It really comes down to whether you like rifles long and lean or more massive and beefy.