This is honestly way too hard. All of these names are wonderful, and I actually have all of them on my list. Truth be told, each name sounds great with your kids names, which just makes this even harder. I'll try to not be so confusing with this answer.
First up: Dean. In my previous answer, I told you how much I love this name. It's strong, short, sweet, simple, and stoic. It sounds so brave and courageous and makes me think of a charming, cheeky boy who has a huge personality. Alexis, William, Colin, and Dean could most definitely work. Plus, Dean Jonathan is actually really adorable. I think this name is nearly perfect with your other kids.
Next is Jack. A to-the-point, stand alone name that has been used for centuries without a hitch. It's a good way to honor yourself since you and your wife honored her (your wife) with your daughter's name. As you pointed out, Jack is a nickname for John, and your name is Jonathan, so it works well. Instead of using Jonathan as Jack's middle name, you could easily make Jack his first name and choose a different middle name for him. All in all, this is a great name with a ton of class and character, and it works well with Alexis, William, and Colin, but I still like Dean more.
Now, we're up to Joel. A name very similar to both Dean and Jack. It's a one syllable name that hasn't been used much, and it's potential as a contender in the top one hundred is dwindling. Take that as a blessing! This means that your son may be the only Joel he ever meets! As I've pointed out before, you definitely have a little "Jon and Kate Plus 8" thing going, but I still really like this name.
Here's the toughest one for me to describe: Samuel. This is my second favorite boy name, and it's been in my top ten ever since my fascination with baby names began. There is something so wonderfully amazing about this name. It's historical, timeless, classical, handsome, masculine, and downright adorable! The nicknames Sam and Sammy honest to God make me melt inside, and I so want to use this name on my own son (if and when I ever have one). Seriously, I love this name so much. Alexis, William, Colin, and Samuel work perfectly together! Gorgeous and stunning!
Last is Andrew. This name is my third favorite to go with your other kids names with Dean and Samuel being tied. I think Andrew works really well with Alexis, William, and Colin, and there's absolutely nothing wrong with having two A names, especially if one is a boy, the other is a girl, and their names sound and look nothing alike (now, a name like Alexander is a different story). This is a brilliant name that automatically makes me think of a goofy, well-rounded young man.
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My two favorites are Dean and Samuel. I'm honestly leaning more toward Dean with your kids names, but some part of me keeps screaming that Samuel fits better. Still, I think Dean would add a TON of flare, sophistication, and sweetness to your other kids names. Either way, Dean Jonathan or Samuel Jonathan sound great no matter what!