Heatsinks placed on top os a A4988 chip are not very effective. These chips are designed to be cooled via the thermal tab underneath and thence by the PCB. The plastic case of the chip is not a good thermal conductor.
Unfortunately, stepstick PCBs are too small to do a good job of conducting the heat away. However, you can get improved boards with 4 layer PCBs that do it better, such as the Ice Blue stepsticks from T3P3. All-in-one controller boards do a better job of cooling the chips because they have more board area.
There are a few stepstick designs that put the chip on the underside and the heatsink on top, with thermal vias to conduct the heat from one side of the board to the other. Those should work quite well, especially if you use a fan to blow air on the heatsinks.
Unfortunately, stepstick PCBs are too small to do a good job of conducting the heat away. However, you can get improved boards with 4 layer PCBs that do it better, such as the Ice Blue stepsticks from T3P3. All-in-one controller boards do a better job of cooling the chips because they have more board area.
There are a few stepstick designs that put the chip on the underside and the heatsink on top, with thermal vias to conduct the heat from one side of the board to the other. Those should work quite well, especially if you use a fan to blow air on the heatsinks.