I tend to say "Suffice it to say" and think this may be more grammatical as it is the subjunctive form of the phrase "it suffices to say".
Both seem to be acceptable though and from a purely usage viewpoint, Google has 15 million hits for "suffice it to say" and 13 million hits for "suffice to say" so popularity seems to be fairly equally divided.
'Suffice it to say...' is certainly the earlier version, being first recorded in the 1790s. 'Suffice to say...' is a more recent simplification. Nowadays, it does not really matter, as you say.
I should have added above that, as Calibax says, 'Suffice it to say...' is a variant of 'Let it suffice to say...' It is subjunctive and not a corruption of 'Suffices to say.'
"Suffice it"
is correct - it is a third person imperative, translated as " let it suffice", and can only be expressed as a subjunctive.
(Much easier in Latin)