If the use of arxivarXiv in your field of science is common, that is probably the better option for you personally. For example, subject specific abstract indexing services (like inSPIRE or ADS for high energy physics and astronomy) will automatically link their entries for the arxivarXiv version to the journal version. Consequently, you will easily be able to obtain combined citation counts.
However, there are some limits to the arxivarXiv. One of the foremost is that they accept pre-prints only for a limited number of subject areas (essentially physics+astronomy+mathematics+(some) computer science with maybe some cross-over into other fields). Consequently, for some fields the arxivarXiv simply is not an option. (There also some subfields for which the arxivarXiv would accept pre-prints, but the use of the arxivarXiv is not so common). In this case, alternatives could be interesting.
Personally, I have never heard of preprints.org. One potential worry I would have is that it is owned by a (commercial) publisher. So, even though it is currently run as a non-profit with free access, I am not sure what safeguards there are against them changing their usage policy in the future. I would certainly try to find out before submitting anything.