Looks like my onboard NIC doesn't support VLAN tagging.
I set up LAN and opt3 identically:vlan.png
intelvlan.png
When I have my desktop directly plugged into em1, I don't get an IP from pfsense.
When I have the desktop plugged directly into igb1, or igb1 through the switch, I am able to get an IP from the VLAN.
I still haven't figured out the TomatoRouter part, but atleast I know now it's not a pfsense issue.
My motherboard: https://www.supermicro.com/products/motherboard/Xeon/C216/X9SPU-F.cfm
Network Controllers
Intel® 82574L Dual Port Gigabit Ethernet
Virtual Machine Device Queues reduce I/O overhead
Supports 10BASE-T, 100BASE-TX, and 1000BASE-T, RJ45 output