If you’re going for strict historical accuracy, a 1990 PC could have had either MS-DOS/PC-DOS 3.3, MS-DOS/PC-DOS 4.01, or DR DOS 5, along with Windows 3.0. MS-DOS 5 was released in 1991, and DR DOS 6 followed in the same year. An interesting OEM option is Compaq’s 3.31 DOS, which included support for partitions larger than 32MiB, and the first expanded memory manager (CEMM).
Of all those options, I’d say DR DOS 6 is the most convenient: it has the most memory optimisation features of the lot (Compute Magazine, June '92 review). You could also try MS-DOS 5, perhaps with QEMM or DOSMAX if you need more conventional memory. (You’ll need a boot menu anyway because many early nineties games aren’t compatible with V86 memory extenders.) Both of these would be period-accurate for 1992.
If you’d rather go for convenience, your options widen: you could use MS-DOS 6.22, OpenDOS 7.03, or FreeDOS. All three are pretty much on a par in terms of usability: while FreeDOS has better tools, you’ll find far more information online about MS-DOS and to a lesser extent OpenDOS. (All three include good documentation of their own.)
While on the subject of convenience, I’d also recommend going for Windows 3.1 or even Windows for Workgroups 3.11: they’re not historically accurate for 1990 either but they’re much more usable than 3.0. If your reference point is 1992 then Windows 3.1 is fine.
Of course all this ignores the question of licenses. It was also common in those days to install loads of utilities to alleviate the OS’s deficiencies, which levels the playing field too.
I actually bought a PC in 1992; I got a 33MHz 386 with 8MiB of RAM (which was a lot at the time), a 120MiB hard drive, and DR DOS 6 and Windows 3.1. My only regret in the years that followed was not spending a bit more to get a 250MiB drive. I knew someone who had a gigabyte SCSI drive in 1992 but that cost half an engineer’s monthly wage (10 000 FF).