Additional information for this guide has been received from Dines and Megalomaniac.
This guide describes a simple method that can be used by the Cyborg to tax all natives, except Amorphous. While this method will generate slightly less than the maximum taxation from the natives, it is much easier to implement than the maximum taxation method.
For most races, natives are a resource to be nurtured, so that they deliver as much as possible to the colonists. For the Cyborg, natives are a resource to be assimilated and converted into colonists. Because of the limited number of turns the natives will normally be around, it is appropriate to squeeze as much tax as possible from them. As the natives will all be assimilated within a relatively few turns, their happiness can be quickly reduced.
There are four phases to taxation for the Cyborg: Colonist Harvesting, Early Assimilation, Late Assimilation and Colonist Only.
Gnerphk wrote a guide that describes how to extend the assimilation time of natives ( http://www.planetsmagazine.com/races/borg/borgguides/riding-the-wild-serf-or-the-fine-art-of-harvesting-peasants/ ). That guide clearly describes how to harvest colonists from a planet with natives. Once the decision to move to total assimilation has been made, or the number of colonists becomes too large to effectively reduce, it is appropriate to switch to using this guide.
In the this phase, the taxes are limited by the colonists. During this phase, the natives should be taxed as high as possible, with the income just under the number of colonist clans (at the number of clans for Avians), and below 5,000 MegaCredits. Also, when this process starts, the target number of Factories should be set to 999, in an effort to maximize available funds from colonists. Please do not set the tax rate higher than 20%, as those rates will decrease colonist happiness, but will not increase income for the Cyborg.
If the climate of the planet is "cool", "warm" or "tropical" (especially "warm"), and there are over 1,000,000 natives, it is probably appropriate to set target for defenses to 999 as well, as as this will allow the planet to defeat a small or medium warship, even without a starbase.
This phase starts when the native happiness approaches 40 points. The taxation should be decreased so that the native happiness stops at 40 points, and goes no lower. Again, the combined taxation of the natives and colonists should be below 5,000 MegaCredits.
While taking the natives down to 40 happiness points may seem excessively harsh, it should be remembered that the decision has already been made that the remaining natives have no use, other than to be quickly converted to colonists. In addition, if the natives are at or near 40 happiness points, and an enemy takes the planet over, they will receive a planet of rioting natives if they're lucky enough to survive the first turn.
In some cases, it will be advisable to tax down to 31 happiness points. Due to destruction of mines and factories, this will cost 30 MC for each turn where the natives survive. Whether or not this is economically feasible will depend on the number of natives and their level of government.
If the taxation rate has been reduced to under 20% to keep the natives from rioting, then it should be increased on the turn the last of the natives are assimilated, with a goal of 31 happiness points. As the taxation and assimilation happens prior to rioting, the tax will be received, but the planetary structures will remain intact. If the happiness drops to 30 points or lower, the taxes will not be received.
In this phase, there are no natives. The Colonists should be taxed as though they're any other colonized planet without natives. There are numerous guides for this. The one exception is for overpopulated planets.
If a planet is overpopulated, and colonists are dying, colonist taxation should be increased. For the first turn after the last of the natives is assimilated, the tax rate should be increased to cause the colonist happiness to drop to 70 points (limiting income to 5,000 MegaCredits might require this to be done in two turns on highly populated planets). Once the colonist happiness hits 70 points, the colonists should be taxed like a homeworld.