The main difference is they are functionally different.
Why do you want to know? If you need to know to offer a customer the best offering then you already know the major differences, you have to to be able to sell them.
Microsoft acquired these over time, NAV purchased AX prior to Microsft acquiring them.
If you think of these as separate as any other ERP software but with a committment to having a common user interface, platform and stack that would be a good start, but everything else is functional, and that is then subjective to the needs of the customer.
I am constantly being asked (by Prospects, Clients and other resellers) about which Microsoft Dynamics ERP product is best, Dynamics AX, Nav, ect.
I wrote a page that includes Microsoft’s own positioning at;
Hope that helpsMichael