Where can we apply for European Union funding to make our our hotel / destination / attraction accessible for disabled people?

There is no EU office which receives applications and gives direct funding to owners of businesses who want to make their facilities accessible to disabled people. It may be possible that some funding is available for improving accessibility through the EU Regional Funds, which are administered separately by each EU Member State. Each country makes its own programme and priorities for spending EU funds at national and regional level.
Contact, for example, the Regional Tourist Board or Regional Department / Prefecture or Municipality to learn how these funds are allocated at the regional and local level. Possibly they will have a support programme addressing architectural adaptations and accessibility for small enterprises.
There is also a website where you can get more information about European support for Small and Medium sized Enterprises: (SMEs). 
http://ec.europa.eu/small-business/index_en.htm  Search for contacts in your own country.