You seem to be conflating two things, namely whether a journal is online and whether it is open access. I'll focus on the open access part of the question, since whether there's a print edition is basically irrelevant nowadays.
So what will be better, to go through the "standard" (pay-per-view paper journals) or the online free of charge ones?
"Better" is not well defined, but in this case the situation is simple enough that the question can be answered: neither one is better, outside of a couple of specific factors.
Open access journals have one advantage, that anyone can easily read the official published paper, and one possible disadvantage, that there might be publication charges. Other than that, there is no significant difference between open access and traditional journals, at least among respectable journals. There are tremendous differences between specific journals (in prestige, rigor of the review process, speed of publication, etc.), but these things simply can't be predicted on the basis of whether the journal is open access.
I said "among respectable journals" in the previous paragraph for a reason. There are tons of obscure, predatory open access journals that will publish anything for a fee. (They often claim to perform peer review, but it's clear from the garbage they publish that the review process is meaningless. This problem is restricted to open access journals, because you can't make money selling subscriptions to a journal nobody wants to read.) You should absolutely avoid predatory journals, since they will actively hurt your paper's reputation.
If impact factor isn't the key which is better(and faster)-going through the big publishing houses who have a "well-oiled machine" and can handle my request with routine and speed or risking in the online-only community?
You are oversimplifying things by supposing that big publishers have a well-oiled machine. Some do and some don't, and the same holds for small publishers. Furthermore, some open access journals are published by big publishers, and some subscription journals are published by small publishers.
My topic is something quite radical I have been working on it for years now and I have diverted a lot of what is "standard" for this community so I am pretty much a lonely wolf and expect enormous troubles going through the peer-review(radical ideas). So what will be easy for me-the paper or the online journals?
If the difficulty is with peer review, then you can't expect an easy time with any journal worth publishing in (i.e., a non-predatory journal).