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Of course, this assumes you have the scanner room HUD chip upgrade installed on your head equipment slot and easily see the scanner results.
Another possible hint:
Similar depth/difficulty for magnetite might be around 200-300m beneath the floating island. Just have to deal with the warpers, but they are pretty benign once you get use to them.
and if you're scared of reapers, just get a PRAWN with grappling hook: you can pick up the magnetite while in the suit and if the reaper bothers you, you can punch it repeatedly in the face, and.. if feeling particularly vindictive you can use the grappling hook to attach yourself to it and keep punching it until it dies :p
The other mineral commonly available in the dry caves mentioned below is not magnetite, it is lithium crystals.
All other tips in this post remain correct.
Easiest, relatively safest general location for magnetite is Jellyschroom Cave.
In fact, you can often gather enough for initial tool purposes just within the quite safe entrance areas.
Take the Seamoth down there with a couple of Hull Reinforcements, and a repair tool, and kill the first few Crabsnakes by ramming, to make a relatively safe area.
Take the time to drop a Scanner Room nearby. Relay some power from Solar if necessary, or also drop an MPR with a Bio.
Scan. The place is lousy with magnetite.
Next best gathering locale is the dry caves on / in the Mountain Island. That area is also lousy with magnetite, and not too inherently dangerous, but confusing. Don't get lost and die of thirst. Bring some light. Leave some trail markers if you can.
The underwater slopes of the Mountain Island can yield a small amount of magnetite, if you can spot it. Reasonably close to map center, but more dangerous.
All the other magnetite bearing biomes and sub-biomes are further away, deeper, more dangerous, and / or require drilling.
Be aware that by the time you are gathering magnetite, you may be venturing into areas that can ramp an increasing level of Warper aggro/interest. You can't stop this, it is inherent to the game and you can cope, but you can delay it / limit it in the early game by choosing carefully where you explore early. Basically sticking within the areas that the story leads you to early on. That was a factor in my recommendations above.