Landing at Haneda at 11pm

Hello there,

I will be going to Japan this Autumn. I was wondering whether I would be able to catch the last train from Haneda to Shin-Okubo(JR Mainline) station, If my flight lands at Haneda on 11pm. Would that be enough time to clear customs and catch the 12.00am Keikyu Line, and transfer at Shinagawa to get on the JR Yamanote line to Shin-Okubo station?

Since the last train of the Keikyu line departure from the station at 0:02, you will in time for it.
http://www.hyperdia.com/en/cgi/en/search.html?dep_node=HANEDA%20AIRPOR...

It will be rushing.
If you can managed to leave Haneda at 0:00(assuming weekdays), you will be in Shinagawa Station at 0:17 by Keikyu. Yamanote line leaves for Shin-Okubo Station at 0:21 and 0:38 at latest.

Or you need to catch a nigh express bus(operated by Keikyu bus, 2060 Yen/one way) at 0:30, arrive Shibuya West Exit at 1:19, then catch a taxi to Shin-Okubo Station.

If my flight lands at Haneda on 11pm, would that be enough time to clear customs and catch the 12.00am Keikyu Line,...?

If your plane actually arrives at 23:00 to HND International Terminal, you are highly likely to catch the last Keikyu train for Shinagawa (departing at 00:01 or 00:02) and make a transfer in Shinagawa to a JR train on Yamanote Linefs outer loop.

If your plane is scheduled to arrive at 23:00 but is actually delayed much, you may miss the last railroad connection.
(Railroad operators in Japan describe train times mostly by the 24-hour system.)

[By train]

After the midnight when a weekday ends,
the last Keikyu train for Shinagawa is scheduled to depart from Haneda Airport International Terminal Station at 00:01 and arrive to Shinagawa Station around 00:23.

After the midnight when a Saturday, a Sunday or a public holiday ends,
the last Keikyu train for Shinagawa is scheduled to depart from Haneda Airport International Terminal Station at 00:02 and arrive to Shinagawa Station around 00:17.

(The next major revision of Keikyu timetables may take place in October 2014.)

The second / very last JR train on Yamanote Linefs outer loop (for Shin-Okubo) is scheduled to depart from Shinagawa Station (Track 2) at 00:21 / 00:38, regardless of days.

Public holidays in Japan until November 2014 will be
the 15th and 23rd of September, the 13th of October and the 3rd, the 23rd and the 24th of November.

Note
: Also Tokyo Monorail has a station in HND International terminal. You can follow signs for Keikyu.
: The Keikyu fare is 410 yen per adult. The Keikyu and JR fares in total are 610 yen per adult to Shin-Okubo Station, or 630 yen per adult to nearby Okubo Station.
: In Shinagawa, there is a Keikyu-JR transfer gate near Track 1 of Keikyu, where you can exit Keikyu and enter JR at once.
http://www.keikyu-ensen.com/images/station_map_2.jpg
: If you have used a Keikyu-only ticket to Shinagawa, you can purchase your JR ticket (for 200 yen or 220 yen per adult) at a JR ticket vending machine beside the transfer gate.

Shin-Okubo (with the first "O" pronounced long) Station is in Shinjuku City ward. This JR Station is not equipped with any elevator or escalator. It seems you cannot avoid using a staircase there.
http://www.jreast.co.jp/e/stations/e857.html

Alternatively you might hope to use nearby Okubo Station if its north gate is enough close to your hotel. This JR Station is on the route called "Chuo Sobu Line" for Local trains only. There is an elevator between its platform and its north concourse.
http://www.jreast.co.jp/estation/stations/316.html
Logically you can switch via the same platform in Shinjuku Station from your Yamanote Line train (using Track 15) to your Chuo Sobu Line train (using Track 16).
Please note, however, that if you take the last Yamanote Line train, you can choose only the last Chuo Sobu Line train and should change trains within 1 minute.

[By bus + taxi]

The last limousine bus for Shinjuku is scheduled to depart at 00:20. The one-way bus fare is 2000 yen per adult.
http://www.limousinebus.co.jp/en/platform_searches/index/4/214
(Actually Shinjuku Station of JR is apart from "Shinjuku Station West Exit" bus stop, which is in Shinjuku highway bus terminal.)

The bus at 00:30 for Shibuya (mentioned by tokyo friend 48) seems to be the last one of the three night limousine buses co-operated by different companies. Now this bus is operated by Tokyu Bus.
http://www.limousinebus.co.jp/en/platform_searches/index/4/128

If a taxi runs smoothly to Shin-Okubo Station after the midnight,
from near Shinjuku highway bus terminal it needs 10 minutes or less and about 1000 yen per car,
while from Shibuya Station West Exit it needs about 15 minutes and about 2500 yen per car.
It may need a little more time and/or fare depending on the road traffic.

Thank you so much everyone!. This was really helpful. I have to get to the Shin Okubo station as my hotel is within 5 minutes walking distance to the station. Now, I know what to plan, which route to take in case I dont quite make the last train, once I get there.