It will not make a difference in the amount that is actually incurred, but it could make a difference in the amount that is withheld, which could change the amount that you owe or the refund you get when you file.
Bonuses and other non-recurring income are withheld at a flat rate, while recurring pay is extrapolated out to a full year and withheld as if that were your total income for the year (less any exemptions depending on your tax status and dependents). Bonuses to not take exemptions into account since it's assumed that your exemptions are accounted for in your regular pay.
So if you had a bi-weekly paycheck that included a large bonus, you could have WAY too much tax withheld, since the tax tables would assume that you'd get that same amount in EVERY bi-weekly paycheck.
It won't be perfect, but it's more accurate to just have the bonus paid separately than to lump it with your "normal" paycheck.
It's also possible that your company's payroll system can separate bonus pay from regular pay and withhold for them independently, even if they're on the same paycheck, in which case there would be no difference at all.