I have found a couple control methods that have proved quite effective and human friendly.
The first control product I highly recommend is a food grade polymer called 'Gopher Goo' that when poured into a gopher or squirrel hole and hydrated with water, will in turn swell up to at least 4 times it's size inside the hole and fill the opening and create a long term ' barrier plug' that seems to force the gophers to move on from our job sites. The polymer also contains a small addition of organic compost that helps in the rebuilding process of the damaged roots. The polymer will last up to 2-3 years in the soil before it breaks down naturally ,
There is no toxic ingredients inside this product so it is extremely safe to use around children and pets. The polymer creates a sticky goo all over the pelt of the pest and this creates a big problem for them as the pelt needs to be smooth so that they can move through the holes and tunnels in the ground. The pest are forced to move on from the site since they despise getting the goo on their pelts and we end up managing the pest off our job sites. You can learn more about Gopher Goo at www.gophergoo.com.
The next pest management product that I have had really great success with is a cage device called a squirrllnator.
This cage has two openings on two sides of the cage and a cage door on top to take out dead squirrels or release them elsewhere if you choose to do so. I have found the best 'Bait' for the squirrel is orange pieces,sunflower seed, and mixed nuts. This mixture of goodies seem to attract the squirrels into the cage and once they are in there the door they entered is a one way access. they cannot get out once they enter. This cage is a lot better than using poison baits and seems to work fast and efficiently and by using one or both of these management tools in your quest to rid your site of pocket gophers and squirrels, I am sure you will have great success.