Tell them you have another offer, but I wouldn't go into specifics. You can mention that they have PTO as well as paid holidays and that they are offering a higher salary; but leave it at that.
Let Company A know you are very interested in their company and feel as though it would be a good long-term fit, but also mention that it would be hard to walk away from another offer that has better upfront incentives.
While I worked in HR, we were willing to negotiate PTO days in lieu of salary so maybe there is a little more wiggle room there than they let on. PTO and Holidays are golden and pricesless IMHO; you need to be able to have time off.
Maybe you should quantify the differences between the companies to come up with what you see as a fair counter offer. Total up the cost of benefits as well as the PTO and holidays plus/minus the salary difference and see where you stand.
Good luck and let us know how it goes. People always ask questions and never update.....