I've had this same problem with shoes for years because I have a slightly wider than normal forefoot. Here's what I do.
1. Wear a thinner sock.
2. Put in a thinner insert.
2a. Trim off the outer edge of the insert in the toebox about 1/8". In most shoes this insert actually extends slightly up the inside of the toebox, taking up unnecessary room.
3. Skip the bottom eyelets entirely. Or in one or two cases, I've skipped the bottom two sets of eyelets. They're unnecessary if the shoe is already snug in that area.
I do all the above steps in almost every pair of shoes I own. When it's not enough, I'll add the following steps.
4. Cut a slit in the shoe about 1 inch long starting roughly where the bottom lace would be (but you've already removed it in step 3). Cut through the tongue, and the cross piece of material that sews the tongue to the front of the shoe and continue cutting into the mesh on the top of the shoe. The cut should be roughly in the middle of the shoe and runs from front to back. This cut will be almost invisible when you put the shoe on, but it will expand noticeably when you put weight on your foot. You don't need to go more than 1/2 to 3/4 inch into the mesh of the toebox. Cutting that connector strap is going to release a lot of tension and let the toebox stretch.
5. You should probably skip this final step, unless you are confident that you can do it without cutting into the mesh. Some shoes (not all) have a raised rubber rib around the toebox where the mesh upper meets the insole. Use a boxcutter or exacto knife to cut this rib off. Make the first cut as if you were shaving the material off the side of the mesh. Then pull that material off of very carefully cut it off without cutting into the mesh. Continue to do that until you are getting close to the mesh.
6. If there is a leather strap or toe protector that runs across the little toe, cut it off if you can. Carefully cut the threads holding it to the mesh. Lift it up off the mesh, and then carefully cut it off without cutting the mesh. The reason you do this is that the leather won't stretch, but the mesh underneath it can stretch. On some shoes, this toe strap is melted to the shoe itself so you can't cut it off. If you see threads holding it on, it can be cut off.
If this doesn't work, you should throw away the shoes. Running in shoes that are too narrow can cause Morton's Neuroma.