So, as the director of a biodiversity conservation NGO I get asked this a lot. Here’s my take on it.
As a general principle the effectiveness of your donations depend greatly on the amount you’re donating, the size of the organization you’re donating to, and the focus of said organization.
For example, a small donation (@$10,000 or less) will generally be vastly more effective when donated to a small NGO rather than to a large one, and a large sum of money (@$100,000 or more) will generally be more effective when donated to a large organization as a small organization may not have the capacity to take advantage of a large sum of money all at once (although setting up an endowment with those funds to provide constant support for a smaller organization would be very effective too).
In general the smaller NGOs have lower overhead costs and place substantially more of their resources into conservation activities than big NGOs do.
You need to pay close attention to what you want your support to accomplish. Do you want it to benefit something in a highly regional areas or are you more interested in the funds going to support policies and laws that affect a large area?
Are you interested in supporting activities in your local area or are you looking to support activities elsewhere in the world?
Do you have a particular species, ecosystem, or issue you’re interested in?
Enormous volumes of money go to conservation of iconic species (and there is absolutely benefit to that), but there are thousands of Critically Endangered and tens of thousands of Endangered species that receive almost no conservation support, plants and invertebrates are especially underrepresented in the conservation world.
Addressing issues of education, livelihoods, food security, and health are often the most critical and effective tools for biodiversity conservation, but they also tend to the be slowest. Is funding those a priority?
Anti-poaching activities? Lots of funding goes to on-the-ground anti-poaching activities, but that’s not addressing the actual problem, which is demand for said items, which is an education, legislation, and enforcement issue in the countries of the end user, not on the poacher’s end of things. If you’re interested in anti-poaching work, then that’s something to keep in mind.
Sorting out what your particular interests are is the first step in all this and will help you find the key subjects necessary to find an appropriate conservation organization to support.
Until you sort out what it is specifically you hope to have your support accomplish no-one can give you a useful or valid answer as we don’t know what your priorities are.