The question as asked has no real answer, so let me explain a few topics that will point you in the right direction.
The number of gears has no effect on top speed. The ratio of each gear is the important part. You could conceivably have a 3-speed transmission with a higher top speed (for a given RPM) than a 7-speed transmission. Having more gears can give you better acceleration and handling because you can keep the engine in the "power band" more easily. Engines can have a narrow range (power band) where they make the most efficient power.
A larger engine could produce more power, and should have a higher top speed with all else being equal - however the gear ratios of their transmissions are almost certainly not going to be equal, so again, that's what we really need to know.
Since you are asking about two motorcycles with small engines, wind resistance will probably be the biggest factor in top speed. You're not going to make it to either vehicle's theoretical top speed (redline RPM * final gear ratio). The larger engine should be more powerful, and should allow you to eke out a higher speed, but this is just a guess. There's also many cases of a smaller engine having more power than a larger one, so that adds another wrinkle.