One of my players recently asked me about a character idea of a runner that's an animal/critter trainer/handler, he doesn't carry a gun just a simulator/fake with a laser sight that he uses to point with and act as a targeting guide for his attack animals. Sounds like a fun concept, but I'm at a bit of a loss where to look book-wise for something like this.

The Critters sourcebook is the first place I looked but haven't found anything skill wise that would apply other than the failure check for cybered-up animals turning on their handler.
Does anyone know of other books with critter handling rules? Even from 4th edition I could look up and convert?

SR4 - Running Wild might help you out. It has chapters on augmenting animals and integrating them into your game, as well as introducing new skills for that purpose.

Yes, running Wild helps. I used it a lot for my PC in a short-lived outdoorsie campaign here on DS,The Sun Never Sets, whose name was Stogie, and he had a sidekick border collie Jake. Sheep farmer kicked off his land by corporate greed and now tending towards eco-terrorism.

You can find the build HERE.

Well, you can issue a common command to a cluster of drones, so you could subscribe an entire swarm of Ares Felix the SynthCat (SSG.122) to your RCDeck and tell them to chase the laser pointer. That's the first thing that comes to mind.

It sort of sounds like a Ranger from that other RPG (the one in which Vin Diesel's ranger is named Riddick) in which case, the Awakened route is probably the cleanest. Get the player to generate as a Conjurer, a Mystic Adept, or a Full Magician, spend as much of their Resources as they can on buying Spell Points up to 50, then use those to Initiate (Magic in the Shadows) with a Familiar Ordeal (ie this first pet does not cost 1 Magic). "In addition to the standard uses for Spell Points during character generation, gamemasters may allow player characters to use Spell Points in place of Karma Points in order to begin the game as an initiate, to summon and maintain an ally spirit, and so on." (SRC.15) This Familiar (MitS p60, p107) will invest any mundane Critter, raising its physical attributes by the Spirit's Force, bringing Sapience and a bunch of other benefits. You can grant it any Active/Knowledge skill the summoner has (Stealth, Etiquette, Electronics, etc.) During play, the character can acquire additional Critter vessels and summon into them additional Ally spirits, each of which will cost 1 Magic and a bunch of Good Karma. When other characters start slinging spells or lead, this character commands the Ally spirits to accomplish specific tasks, and they intelligently go about doing so using the Critter's body to interact with the world. Skillwise, the Ally/Critter hybrid would use its Force or its Reaction with no Defaulting penalty. They don't run out of Services, but they can be Banished, killed, trapped behind Wards, etc.

4th Ed has the stirrup interface which is used to make biodrones. It's the next step beyond Snake-eyes from 3rd Ed. So if you were willing to port stirrup interface, you could consider each animal companion to be a biodrone. Rigger 3 p62 would tell you the effective Bod of a biodrone of that size, and you could perhaps add a point of Vehicle Armour if their Critters entry lists Dermal Armour. You could give them Autosoft Interpretation so that you could chip them with Clearsight and Sharpshooter, and maybe give them some kind of cyberdart or cybereye-laser weapon or something.

If memory serve, there is a set of rules for adepts attuning some animals in SOTA 63 or SOTA 64… Maybe worth having a look.

It looks more like what OP's player wants than a familiar I think.