i have experienced this issue when i was new to the route going for a project within this part of west Africa, so let me help you out on your questions:
1. yes you can get a flight from Lagos to Niamey (Via Abuja or Lome), Airline? Asky Air. they are affiliated with Ethiopian Air. the flight will be from Lagos to Abuja or Lome/Togo and then to Niamey. check the website of the Airline: http://flyasky.com
you can also fly with Air Burkina, but you have to get this through an agent cos you will a flight from Lagos to Accra/Ghana with Air Nigeria and then Air Burkina from Accra to Ouagadougou/Burkina Faso and then Ouagadougou to Niamey (Although you might spend 12hours in transit in Ouagadougou, Airline will lodge you in a hotel on their bill)
2. considering traveling by bus? well not a bad idea but long i will tell you cos i have used that too. if you consider that, then i will prefer you either take a bus from Lagos to Accra/Ghana (preferable ABC transport, the best with comfort from Lagos to Accra) which should be an 8hours trip. then from Accra to Niamey (the bus service i know through this route is 'great imperial express') which should be a 30 hours trip. i prefer to use from Accra to Niamey, but there are also lots of bus services going from Cotonou/Benin or Lome/Togo to Niamey but i have never tried from these locations. but if you intend using this location, then you also take the ABC as it also goes to these locations and from there you take a bus to Niamey (duration of trip is almost 30 hours also). i can also say the route is relatively safe as i have had traveled this route by bus with some Europeans in the bus too.
3. there are bus service going from Niamey to Gao, the ones i know are Sonef tansport, Rimbo transport and Air travelers. i cannot tell of the safety or comfort because its a route i have not been to
4.Mali is presently in a political crisis now and Timbuktu in particular is experiencing crisis, so i cant say much about this.
hope i have helped in my little way to give guidance on how to get to Niamey from Lagos.
Moctar and Mark, thank you both for your thoughtful responses. You are both well-versed!
I enjoy road travel, and I'm thinking I should plan a full West Africa road trip for the future-as a tourist.
I have to skip Niger, since I can't get a visa here in South Africa, and it will take over a week to get it in Abuja.
So now I'll just fly from Lagos to Bamako. I've spoken to a few Malians, and if it's relatively safe (I'm a journalist who's okay with taking calculated risks) I'll travel North.
Mark, I've tried Asky, Air Nigeria, Arik Air, Ethiopia Airline, Kenya Airways (flight price is ridiculous) Cameroon Air, all of which show up on flight search engines. But when I'm on their sites-nothing.
I'll hand it to a travel agent to book the flights.