@Gabe N. - EVICT or CFK. Do it yesterday.
My last tenant had a dog who I think was pooping on the floor. I didn't see any urine but on the occasional visit I would see poop on my (BRAND NEW HARDWOOD) floor. Then they stopped paying on time. I started the eviction process twice, and they knew the game -- if they paid the rent/late charge/legal fee before the court date, I couldn't evict. I tried to CFK multiple times, they would skirt my conversations or not answer the phone, or not answer the door, or say they couldn't talk unless the other tenant was home. All the runaround. Then when their lease ended (mercifully), I had a house that smelled like stale dog poop and I am fairly certain it attracted mice, who would then die UNDER MY SUBFLOOR and it added to the smell. Long story short, I decided to cut bait on the house because the numbers didn't work, but also the underlying smell problem would prevent me from now renting to another tenant. I refused to put in thousands of dollars to try and correct a whole house smell problem, which would have included ripping out destroyed hardwoods and subflooring.
@Account Closed made a great point about the problem with dogs (and cats in some cases) are the owners. I love animals, but the MOMENT you caught ANY issue -- OUT. OUT OUT OUT OUT OUT. I too will likely NEVER allow pets for the same reason. They are not mine and I cannot trust their care and upkeep will be given the same attention I would give them.
Your other tenants have ALREADY complained. You have a costly reno on the horizon. Do you not see the atomic bomb slowly exploding in front of your eyes? Your bad tenant WILL spiral because they continue to allow this problem to occur (and I think its a signal they've lost control of their lives, in some way), they will continue to pay late or not at all, then you have a hostile tenant refusing to leave because you are a PUSHOVER. Your other tenants will either get angry about the dog barking and take it out on you, in the form of non-payment or worse, and then the SMELL will permeate from there.
I'm begging you...learn from my mistake. In a few months you will have an EMPTY residence, a major renovation needed, un-rentable units because of a permeating smell, and the bank wants their mortgage payment on the first of the month.
Gabe, I hope you don't take this as a rude response. But if I knew you, I'd give you a swift slap across the face -- this is TOXIC, both literally and figuratively. You need to take serious action, and should have already done this at the first sign of trouble. A dog who poops on the floor once is not going to fix the problem itself. A cat who marks their territory might as well be out on the streets because THEY WILL DO IT OVER AND OVER AGAIN.