To find the unit rate of muffins per cup of almonds, we divide the total number of muffins by the total cups of almonds used.
Manny makes 36 muffins and uses 4 cups of almonds:
\[ \text{Unit rate} = \frac{\text{Number of muffins}}{\text{Cups of almonds}} = \frac{36 \text{ muffins}}{4 \text{ cups}} = 9 \text{ muffins per cup} \]
Thus, the correct answer is:
9 muffins.