Three databases : one instance or three?
The only benefit to using three separate instances would be if you plan to take one instance offline for some reason, e.g. to patch SQL Server one instance at a time, without affecting the other two databases. Of course this doesn't buy you isolation from other types of events, such as patching Windows, never mind that all your eggs are in one VM's basket, too - so all three databases will be vulnerable to underlying hardware issues, resource limitations, etc. whether they are on one instance or three. And of course all three instances will be sharing the same resources within the VM; there is significant overhead involved with running each instance regardless of the databases or volume.

Also, using separate instances - and especially separate VMs - seems to fly in the face of your overall mission (consolidation).

So, I strongly recommend you create a single instance, and put all three databases on one instance.