There is a lot of other stuff to factor in.
First and foremost, are you happy and do you see a future for yourself there? If the company's primary focus is software, then defense is less of a concern than if software is adjunct to the core business. Do you drive profit, or are you a cost center?
Are there people there you can learn from? It sounds like the company is doing well ($166k to $500k profit per employee--profit, not revenue), but if you are 2 years in and already the biggest fish in the pond, then you may have a decision to make, possibly based on whether you can get any equity or not. The small size of the company is a plus, particularly if they are software focused.
If you have any ambition or dream to move to a commercial company, now is probably the time. While defense can provide a premium (especially in the NoVa market), it also tends to come with a bit of a stigma around process that can be hard to shake if you are immersed in it too long (both in terms of habits and perceptions those outside the industry can have). Take your experience and make the jump to an industry that suits your tastes. Loving what you do and sticking with it can yield better financial outcomes than can simply trying to optimize a situation that is "just a job".
If your current company is growing, and you are growing with it, and if you see some of the shared upside...then don't worry so much about base rate. Your skills and ambition will keep you a big fish in that pond and you should start to see the upside soon.