If you have a single mic position it's easy, just stick ReaTune on it (increase the window size for low instruments) and put it in auto-mode (you may need manual mode for some notes though). Reaper uses the same tuning algorithm whether you're using ReaTune or pitch envelopes, you can set the default algorithm in the project properties. I find Elastique efficient gives the best results, I get artifacts with nearly all the others. Sometimes a note doesn't need any tuning, when you have this lucky situation you can bypass ReaTune via automation. If you have a sample that has a steady pitch but it's the wrong pitch (a little bit flat or sharp perhaps) then rather than using ReaTune you could adjust the media item's pitch using the pitch item down/up actions, then you can use the convert pitch to rate script to get higher quality tuning (this script is available in ReaPack I think, it doesn't come with Reaper).
Now multi-mic samples are a different, evil, horrible beast
You can't just stick an autotune plugin on each track because they all work via FFT and will screw up the phase relationship of all the samples so you'll get some nasty chorusing between the mics. Apparently there's a version of Melodyne that can work with multi-mic recordings but I haven't been able to fit Melodyne into my workflow and I don't really want more proprietary software than necessary. So there are only two solutions I have found and they both require some manual work. X-Raym made an awesome script that is basically auto-tune using item pitch envelopes, and there is a script to copy pitch envelopes between items. So you put the script on one mic, tune the samples, and copy the envelope to the other mics. It still uses FFT but because all of the tuning points will be the same it doesn't create any noticeable chorusing. Although the script is automatic and can be used on multiple media items at once, it isn't 100% accurate and you will need to go through the samples one by one and adjust the pitch envelope as necessary (many won't need any adjustment, or very little). I tuned a few thousand samples this way last month. The script isn't free, you can get it from here - https://www.extremraym.com/en/downloads/reascripts-envelope-based-pitch-corrector/.
Now the other method, that I have yet to try in production: Paolo from Fluffy Audio informed me that you can tune a mic position with Melodyne, then rename the file so Melodyne can't find it, and then point Melodyne to a different file of the next mic position. Melodyne will then apply the tuning it applied to the first file to the second file. So I figured why not do the same thing with ReaTune, and in my brief tests it seems to work. You have to use manual mode, tune one media item (best to do this before cutting the samples) then swap the media item for the next mic position and ReaTune should apply the same pitch adjustment. I only did some quick tests with this but if it does work I think it will be faster than Raymond's script for sustain samples but perhaps not for short samples.