This would certainly be linked to the Turkish and Mughal conquest of the subcontinent.
In pre-medieval India, the academia was heavily dependent on royal patronage, as the Brahmin and Buddhist scholars were attached by occupation to the court. In this period, there had been various mathematical and philosophical advances though there seems to have been a dearth of equipment and tools required for experiment that are fundamentally important to the development of the scientific method. Also, as the accepted answer points out, the printing press which enormously fueled the scientific revolution in the West, was absent in the present case.
With the arrival of the Muslims1 however, royal patronage to the indigenous academia ceased; and later (to a minimal extent) replaced by scholars of Central Asian origin. If an active interest in indigenous intellectual institutions were taken by these rulers, I think the scenario would have been markedly different.
Therefore, the reason for the lack of scientific development in the subcontinent may have not been that it "lagged-behind" as much as that there was discontinuity and in fact a total cessation of the thousand year old tradition of Indian scientific2 thought.
1 A loose term used here to denote the succession of Central Asian empires that entered the subcontinent.
2 Denoting here the various fields of study that might have led to the development of a scientific method.