What you are aiming to do is... it's an issue in methylatioin studies that is not really discussed or even performed (although I am sure that some Smart Alec reading my answer will go out and trawl the WWW to find some website or 'publication'' where it is very much discussed). The reason is that, unlike gene expression studies where it makes sense to summarise, for example, probe values to gene level, it does not quite make sense when it comes to methylation.
Methylation at different parts of the gene (in genomic co-ordinates) could have very different effects on the resulting transcription of the gene. So, whilst they may each regulate the gene, they do so in different ways. Some of the probes included on the commercial arrays may not even have any baring on gene transcription, or at best minimal.
Even if you wanted to summarise these to gene level, you don't require any 'tool' to do it. Just use a summarisation function, like min, max, mean, or median. In R, you could just use
aggregate(). Be aware of the biological interpretation / meaning of doing this, though.