I have the opportunity to receive my salary as a "contractor" self employed or as an employee of the company, bottom-line after taxes, which way will leave me more money in my pocket?

This all depends upon just how many legitimate deductions you will be able to claim on your taxes at the end of the year.

Obviously the contractor will leave you with more money in your pocket since no taxes are being taken out. But you will be responsible for paying your own taxes on a quarterly basis. So you will have to do a lot more work taxwise.

However, an independent contractor may be able to take advantage of more deductions.