If it were me, I'd go with the 3.50 x 10. I linked an old thread, with a chart that may help.
90mm = 3.54", so the 3.5 is much closer to the same width. The chart shows a 3.50 x 10 measuring .9" taller than a 90/90-10. This means it's 2.83" larger in circumference, or in other words, will cover 5.5% more ground, with each revolution. This means the scoot will be geared slightly higher....may not be a good thing on seep upgrades, but nice on flat ground.
The 3.00 x 10 is much closer to the 90/90-10 when it comes to overall height and circumference, but a half inch narrower. No change in gearing/performance, but may have a lower load rating.
Check out the link.
http://scootdawg.proboards.com/thread/32533/tire-sizes