Bring it up calmly and professionally. As a leader, I would also no throw the employees under the bus, but rather take responsibility for bringing up the subject:
You: Bob, I'd like to talk to you about Puppy1 and Puppy2 (using their names makes it more personal, and genuine, in my opinion). I'm a dog person, and I absolutely love them, but it is my professional opinion that their presence in the office is disruptive to the staff. I honestly think that the office is not a good place for them to be when people are trying to conduct business over the phone, or have to focus on their tasks.
Bob: Oh? But Puppy1 and Puppy2 are very well behaved, and they hardly cause any fuss at all! Why, has someone come forward to complain?
You: Bob, as a dog lover, and their owner I think you may have some personal bias regarding the matter. As someone you trust, please believe me when I tell you that I've seen signs of disruption, otherwise I would not be bringing this up. We should work together to find some way in which to separate them from the staff, and to remove the element of distraction.
Now, obviously I'm not privy to the relationship you have with your boss, or how well he might take the conversation, but staying polite, and putting an emphasis on wanting to work with him, not simply blaming him, and walking away are the key points here.
Also realize that completely removing the dogs from the premises might not be possible - at least not right away. Maybe set up provisions to set them up in a side room, in the beginning. If barking, etc. is an issue then you may wish to insist that they be removed from the premises, although that might be a touchy subject.
When it comes to walking them, maybe establish some protocols that one of the junior staff members (an assistant) could take them out without disrupting your meetings, etc? You could throw a line into your conversation about it:
I'm especially concerned about how sometimes we postpone critical conversations in order to meet their needs. In my opinion taking them for a walk should really take a back seat to reaching a decision on X.