My stock answer when asked about any kind of tool is this: whatever software or service you actually use correctly and consistently is the best one.
I realize that seems like a glib answer, but it is fundamentally true. Most of the solutions available will do the trick as long as you actually use them.
In the case of bookkeeping software, the most popular among small agencies are probably Quickbooks, Freshbooks, and Xero. They each have their pros and cons.
My suggestion is to always ask your bookkeeper and/or accountant what package they recommend (and/or support). You might as well make it easy on the people doing the actual work with the program. If your accountant is set up to work with the raw files from whatever solution you pick it can make the annual process of closing the books and doing taxes a little easier.
There are also services like Bench that can do a nice job of handling the entire process for you. Those services are worth a look if you don’t already have a true bookkeeper (usually as a contractor, but sometimes as a part-time employee or as part of another employee’s role).
As with any tool, make sure you are clear about what you need before you go shopping. It is easy to talk yourself into “needing” all sorts of bells and whistles after you watch a demo — and those usually end up being things that you never use.
