I am going to replace a 60amp meter base with a 100amp meter base with an outside disconnect. The main service breaker box is already a 100 amp. The question is, if I ground the outside disconnect and run 4 wire to the main pannel should the main pannel stay bonded like it is now?

Once you relocate the Main Disconnect, the grounding the neutral must be relocated also. In the panel, there is probably a Main Bonding Jumper, either a strap or a screw, that connects the neutral bar to the panel box, remove this jumper.

Also, if your branch wiring is Romex, with bare or green equipment grounds, these all need to be removed from the neutral bar and connect to an equipment bar that is bolted directly to the panel box.

Only neutrals are connected to the neutral bar, and be sure the bar is isolated.

Grounding the neutral only occurs at the Main Disconnect. There can be no connection between neutral and equipment grounds anywhere else in the system.

Are you all set with ground rods, grounding or bonding water lines, etc.