To respond to some things you said:
I've gone back to school to pursue a degree in comp sci and have completed all the necessary pre-reqs for graduate school.
I've run into a problem with the letters of recommendation requirement for the grad program.
... almost all of the comp sci courses I've taken were online
So I take it that negates what I was going to suggest -- that you go to your counselor (at the school where you're taking your CS degree) and ask for his/her advice. Perhaps this should be chalked up to another mark against online degrees.
The college states that the letters need to come from someone who is qualified to assess you abilities with the field. I have no idea who to turn to for letters.
There is no one, if you can't get in actual contact with the instructor of your online course. You might need to build a portfolio (and real human contacts)
So my dilemma is this:
do I just finish the BS degree and get a job
or should I do enough of the undergrad courses to get in with professors and have the letters for grad school.
I recommend you make a Decision Grid. See FAQ 70 (you can get to this forum's FAQs on this forum's "Getting Started" section).
And you need to have your wife chime in on the making of the decision grid.
I should also add that at my current job I get tuition reimbursement so most of the courses would be free. Thus I would like to stay at this company for as long as needed to get the reimbursements.
You should also add this ethical question into your decision grid, then. Most companies would rightly expect you to stay for a couple years after taking advantage of the education benefit.