The error is harmless but to get rid of it, I think you need to break this restore into two commands, as in:

dropdb -U postgres mydb && \
 pg_restore --create --dbname=postgres --username=postgres pg_backup.dump

The --clean option in pg_restore doesn't look like much but actually raises non-trivial problems.

For versions up to 9.1

The combination of --create and --clean in pg_restore options used to be an error in older PG versions (up to 9.1). There is indeed some contradiction between (quoting the 9.1 manpage):

--clean Clean (drop) database objects before recreating them

and

--create Create the database before restoring into it.

Because what's the point of cleaning inside a brand-new database?

Starting from version 9.2

The combination is now accepted and the doc says this (quoting the 9.3 manpage):

--clean Clean (drop) database objects before recreating them. (This might generate some harmless error messages, if any objects were not present in the destination database.)

--create Create the database before restoring into it. If --clean is also specified, drop and recreate the target database before connecting to it.

Now having both together leads to this kind of sequence during your restore:

DROP DATABASE mydb;
...
CREATE DATABASE mydb WITH TEMPLATE = template0... [other options]
...
CREATE SCHEMA public;
...
CREATE TABLE...

There is no DROP for each individual object, only a DROP DATABASE at the beginning. If not using --create this would be the opposite.

Anyway this sequence raises the error of public schema already existing because creating mydb from template0 has imported it already (which is normal, it's the point of a template database).

I'm not sure why this case is not handled automatically by pg_restore. Maybe this would cause undesirable side-effects when an admin decides to customize template0 and/or change the purpose of public, even if we're not supposed to do that.

The id field in your ny_stations table does not seem to be defined as a serial, so it is expected that pg_get_serial_sequence will return nothing.

The duplicate you get relates to one of the records in your SELECT DISTINCT ... FROM ny_raw_trips ... is returning two rows with the same id:

SELECT start_station_id, COUNT(*) FROM (
  SELECT DISTINCT start_station_id, start_station_name, start_station_latitude, start_station_longitude
  FROM ny_raw_trips
  WHERE start_station_id NOT IN (SELECT id FROM ny_stations)
  ) a
GROUP BY start_station_id
HAVING COUNT(*) > 1;

You could list the rows that are introducing the duplication like this:

WITH src AS (
  SELECT DISTINCT start_station_id, start_station_name, start_station_latitude, start_station_longitude
  FROM ny_raw_trips
  WHERE start_station_id NOT IN (SELECT id FROM ny_stations)
  )
SELECT *
FROM src
WHERE start_station_id IN (SELECT start_station_id FROM src GROUP BY start_station_id HAVING COUNT(*) > 1)
ORDER BY start_station_id;

Edit

Once you find the offending duplicates, should you consider that the first occurrence of each case is good enough (e.g. trivial differences in description or coordinate fields), you can use DISTINCT ON:

INSERT into ny_stations (id, name, latitude, longitude)
SELECT DISTINCT ON (start_station_id) start_station_id, start_station_name, start_station_latitude, start_station_longitude
FROM ny_raw_trips
WHERE start_station_id NOT IN (SELECT id FROM ny_stations)
ORDER BY start_station_id;