It used to be 99 prior to the last 2 updates.
If it has changed since then has not been confirmed one way or another.
I would not be surprised if the number we can store has been lowered as it was rather OP when combined with a Lucky Egg and using the 'no animation' exploit - all 99 could be done with a single egg, with time left over.
TL/DR It was definitely 99, but it might have changed.