I know it makes a more dramatic tale with J going back just at the time of the Boglodite invasion of Earth, but why did they wait so long? There was no ArcNet in place to prevent an attack and Boris managed to make it to Earth well before the invasion which took place 43 years after the events of 1969. I'm looking for an in-universe answer naturally.
It's explained in Men in Black 3 that the Boglodite homeworld is 20 years away. This means that after Boris killed K he travels to his home world. After inciting his people to attack Earth he has them travel back and attack Earth. In total it takes Boris 20 years to get home and another 20 years to get back to Earth with the Boglodite army so that explains the 40ish gap in years.
The boglodites invasion starts when agent J is about to time jump. It doesn't make sense for them to wait 40 years to invade Earth in the the new reality (after Boris succeeds to kill agent K and steal the arcnet) especially when we hear that they would starve to death before finding another planet to consume in case they fail to penetrate Earth. This reasoning is confirmed when we know that in the original timeline they are extinct 40 years ago, which means they were already very very hungry at that time and couldn't have the luxury to wait few more years.
Correction: This is explained if you listen very carefully. The boglodites planet is 20 lightyears away from earth, meaning, it would take Boris 20 years to get back to his planet and then another 20 to return ot invade Earth equalling 40 years.
Although it's not really a movie mistake that's the best quote I found so far. The main reason 40 years pass is because of the way lightspeed / Faster than light speed travel works. It may take a short amount of time for the ship / person / fleet to get from point A to point B, but time still passes regularly for either point. A good example is this :
In Einstein's special theory of relativity, there is no such thing as "time" in the singular. Time passes differently for different observers, depending on the observers' motion. The prime example is that of the two hypothetical twins: One of them stays at home, on Earth. The other journeys into space in an ultra-fast rocket, nearly as fast as the speed of light, before returning home:
Afterwards, when the twins are reunited on Earth, the travelling twin is markedly younger, compared to her stay-at-home sibling. The exact age difference depends on the details of the journey. For example, it could be that, aboard the space-ship, two years of flight-time have passed - on-board clocks and calendars show that two years have elapsed, and both spaceship and travelling twin have aged by exactly that amoung of time. On Earth, however, a whopping 30 years have passed between the spaceship's departure and its return. Just like all other humans on the planet, the twin on Earth has aged by 30 years during that time. Seeing the two (ex?) twins side by side, the difference is striking.