I'm not sure if PayPal is the best way, but it seems to be the least expensive for occasional transactions and is relatively convenient. I have a Premier account that I have linked to my bank account. After a renter pays a payment, it goes into my PayPal account (less a 2.9 percent processing fee), and I quickly start the process of tranferring the money directly into our bank account. This takes 2-3 days and is free. Since I pay all our rental bills monthly, time is not really of the essence so this delay is acceptable with me.
There have been one or two times where PayPal is "down" and renters have been delayed in making the payment. This freaks me out a little but I have not been able to find a better way to accept credit cards for a tiny tiny business entity like ours. I know there are people who dislike PayPal but the majority of my renters don't mind doing this.
If you are going to accept rentals through PayPal you pretty much have to link your bank account to them (become "verified"), since the rentals are much more high dollar than the average ebay transaction.
Renters who want to pay for a rent higher than $2,000 also have to become verified, and some of them don't like this. $2K is PayPal's lifetime limit for "unverified" transactions. I had one renter this spring who was vehement about not giving PayPal his bank information. He ended up paying by check. Now I know to disclose to renters who wish to use PayPal that they may have to become verified if they wish to pay the full amount with a credit card. Some of them have opted to use PayPal for the deposit and send a check for the balance and it has worked out just fine.
Also, since $2K is paypal's lifetime unverified limit, if they have already paid for $750 worth of goods on ebay using PayPal over the past decade, they may not be able to use PayPal for a rental deposit without linking bank account information.
When dealing with renters I try to disclose as much of this kind of thing as is practical so no one runs into any surprises.
If there is a better solution than PayPal, I would love to hear about it!