Depending on how much you plan on moving about the country, with a family and a 3 year old, I would think an apartment would be better suited for your situation. You'll have your privacy, you won't share a bathroom and you have access to amenities like a kitchen and possibly a washer/dryer. Whether it's the best value, only you can answer as we don't know your budget, how long you'll be on your trip and how often you'll be changing locations.
Never been to Croatia, but would venture to say a penzion is similar to a pensione. Meaning it's a small, mom and pop-owned guesthouse type accommodation. It won't have all the amenities you might find at a big hotel, it may or may not include breakfast, and the rooms may or may not have private bathrooms.
You may also want to look into hostels. Many hostels now offer family rooms - and some hostels do have rooms that have an ensuite bathroom so you don't need to share. Hostels can give you access to a basic kitchen if you don't want to eat out all the time, and many have laundry facilities.