The difference in area is pi*(6^2-3^2), or pi(36-9), or pi(27). This is approx. 84.82 square inches.
Price per square inch: small pizza: $3.50 / [pi*3^2] = $0.124 / square inch
large pizza: $11 / [pi*6^2] = $0.097 / sq. inch
Thus, the larger pizza is the better deal; its cost per square inch is the lesser.