Should I get a coax or cat5 WAN connection from the ONT?

Verizon's standard install is coax from the ONT to the Actiontec router. This reduces installation time since only one cable run to the router is needed and coax needs to be run to the router anyway for FIOS-TV.

Coax
One advantage of a coax install is that the Actiontec router can be placed anywhere there is an active coax connection.

The disadvantage of a coax install is that if the router fails, your internet service (including VOD) is out until Verizon can ship you a replacement router.

Cat5
With a cat5 connection to the ONT, you can use the Actiontec as your primary router or you can run your own router. If you have FIOS-TV there are a number of considerations in using your own router. See the following FAQ:
»Verizon Online FiOS FAQ »What are the tradeoffs between the various router configurations

Cat5 WAN connections also tend to have slightly lower latency than coax WAN connections.