When figuring income from Social Security, do I use the figure in Box 3 or the gross figure in Box 5 before medicare part B was deducted?

You do not "figure" it out-----you just enter your SSA1099 exactly as it appears.  The software will do all of the calculations.

 Go to Federal> Wages & Income>>Retirement Plans and Social Security  (SSA1099 and 1099RRB) to enter your SSA1099.

On your tax return you only enter the amount shown in box 5 of the Form SSA-1099

To enter Social Security benefits reported on form SSA-1099

Click on Federal Taxes (Personal using Home and Business)
Click on Wages and Income (Personal Income using Home and Business)
Click on I'll choose what I work on (if shown)
Scroll down to Retirement Plans and Social Security
On Social Security (SSA-1099, RRB-1099), click the start or update button