The question comes up fairly often — some jobs are even offered as one or the other — the physician can choose to be a W-2 employee or a 1099 independent contractor.
First of all, I would recommend that you don’t make this a huge factor in your job hunt. The after-tax, after-benefit difference between the two offers is unlikely to be very high.
As a general rule, you should have a higher salary as an independent contractor than as an employee. How much higher? Enough to cover the loss of benefits and the additional payroll taxes.