It depends on how you run the numbers. With the 1099 and then an S-Corp you can potentially by pass paying Social Security and Medicare tax on the amount you are not paying yourself as a reasonable salary which is 15.3% unless you pay yourself $137,700 in salary then the amount drops to 2.9%.
Paying your own health insurance as an S-Corp is not deductible on the S-Corp and with the high of income even if you do take Itemized Deductions you will probably not receive a deduction for the health insurance. Also the amount of expenses you would have as an employee (which are not deductible) versus being an S-Corp where you can deduct them.
On the other side you can set up your own retirement plan and possibly put more money into retirement depending on the retirement plan you choose.
You have enumerated the advantages and disadvantages well. There are other factors such as how much freedom you may have as a business owner versus a W-2 employee besides the tax factor.
The possibilities for the highest tax deductions would come with the S-Corp, but some of those deductions you would not have as a W-2 employee.
Part of it comes down to if you would like the additional freedom and extra work that comes with being a business owner.
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