I am not sure the two are comparable. IPFS is open, basic infrastructure to build distributed applications. Basically the foundation for a more distributed web.
It can be easily used to build blockchain solutions, but can just as easily used to build solutions that are completely unrelated to blockchain. For example my company actyx.io is building a solution that is partition tolerant. Different parts of the system have to continue working if there is a network partition. Classical blockchains are not partition tolerant, so they would not work for us.
Another use case for IPFS is archival and distribution of large quantities of data, which again is completely unrelated to blockchain technology.
So I would say if you want to build a blockchain solution and want to focus on the business aspects, one of the higher level frameworks like hyperledger might be best for you. Maybe you can find one that is based on ipfs. If you want maximum flexibility and have a dev team that is fine with a lower level, protocol/library based approach, building directly on IPFS might be the better choice.
For a technology that you want to be around for the next decades, this separation of protocol and implementation is essential.