Am I missing out by not running in 64-bit mode? I'm running an Early '11 MacBook Pro with 16GB RAM.

Currently, OS X Lion runs in 32-bit mode by default, and an important piece of software I use for work requires this mode (Cisco VPN client). Most of the work I do is inside a VMWare Fusion Windows 7 64-bit VM with 4GB RAM. The RAM upgrade is fairly recent, which is why I am bringing this up now. I've also considered pushing the VM to 6GB or 8GB, but I'm hesitant as I thought VMWare might have problems loading up all that memory in a 32-bit space.

Am I missing out on any performance gains by running in 32-bit mode?
Lion is not meant to be used in 32bit mode. Also addressing more than 4GB ram with 32bit kernel is slower (it uses PAE).

If the only reason of using Lion in 32bit mode is the Cisco VPN client (yuck!) there is a way. Here is an article explaining how to use the native VPN client instead - it's for 10.6, but should work. It's a matter of configuration, not of software. And here is a forum post that pointed to thad solution.

About the Cisco VPN 3000 hardware - yes, it works with iOS and native OSX VPN client in IPSec mode, and it's a matter of software update and configuration. You should be running at least 4.7.2P according to the CISCO field notice. It's stated that it's not supported, but it works. Here is another success story. Make sure that you're using at least OSX 10.7.2.

ps. being tight on money is not always bad, It usually makes people more creative and makes them think and learn new things. Direct your network admin to serverfault, a place I'm sure he will get decent help.