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Written solution:

The number has the form $XX99,$ and so the perfect square that is $1$ more ends in $00,$ and so it is the square of a number ending in $0.$ Suppose that square is $a^2.$

In order for $a^2 - 1$ to be a $4$-digit number ending in $99$, the only possibilities for $a$ are $\{40, 50, 60, 70, 80, 90, 100\}.$

Since $a^2 - 1 = (a-1)(a+1),$ we also need both $a-1$ and $a+1$ to be prime. We are then looking for pairs of prime numbers that are right around $\{40, 50, \dots, 100\}.$

Going through all the possibilities, the only ones that work are $59$ and $61$, and so there is exactly $1$ way to do this. The answer is B.