Actually, ANNOVAR provides some splice site information in the "Func" column of the exome/genome reports. If I recall, I believe MutationTaster also takes splice site predictions into account (and MutationTaster damaging predictions are included in the main ANNOVAR report).
Additionally, these are two programs that I am currently testing for this purpose:
I haven't had a chance to complete my testing, so I don't yet have an opinion about those programs. However, they looked like they could be potentially useful.