I believe this is the answer.
Alice has a winning solution
The strategy is below.
The numbers $1,2,...,99$ can be split by their value modulo 7. This gives us 14 numbers that are $0,2,3,4,5,6$ modulo 7 and 15 numbers that are $1$ modulo 7. So Alice first removes a number that is 1 mod 7. Now, we can pair the numbers with each other such that each one is paired with another such that they sum to a number mod 7. We can do this because their are 14 in each 'class' the 1's pair with the 6's, 2's with 5's, 3's with 4's and finally the 0's can be split in half and paired with each other. Each time Bob removes a number, Alice removes one from the corresponding class. Thus, when Alice removes the last number she can ensure that the resultant sum is 0 mod 7.
Edit: Slightly clearer response with strategy.
Alice removes 1. Bob's number will be $0, 1, 2, 3, 4, 5$ or $6$ modulo 7. There are 14 of each (important that this is even). Alice can maintain that the sum is always 0 mod 7 no matter what Bob removes as she can remove something from a corresponding class (0 with 0, 1 with 6, 2 with 5, 3 with 4). Since there are an equal number in each class (and an even number in the 0 class) Alice can always do this. Thus, at the end when she removes the last number she can still ensure it is 0 mod 7.